Contacts of the strand formed by residues 64 - 70 (chain A) in PDB entry 2V32
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A TRP* 3.6 17.3 - - + -
32A GLY* 4.1 5.2 - - - +
33A VAL* 3.5 34.1 - - + +
59A PHE* 3.0 43.2 + - + +
60A LYS* 4.4 2.7 + - - +
62A ARG* 3.6 27.1 - - + +
63A GLY* 1.3 72.3 - - - +
65A LYS* 1.3 70.0 + - - +
66A LEU* 3.6 2.1 + - - +
132A ILE* 6.1 0.4 - - + -
160A ILE* 4.0 15.9 - - + -
164A GLN* 3.9 4.9 - - - +
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TRP* 3.5 47.5 + - + +
27A LEU* 3.4 27.5 + - + +
28A GLY* 5.2 1.6 - - - -
30A SER* 3.7 20.0 - - - +
31A TRP 3.0 10.6 + - - +
32A GLY* 3.2 1.4 - - - -
33A VAL 2.8 28.4 + - - +
63A GLY 5.0 0.9 - - - +
64A VAL* 1.3 72.2 - - - +
66A LEU* 1.3 60.8 + - - +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TRP* 3.5 5.5 - - - -
33A VAL* 3.5 18.6 - - + -
35A PHE* 4.3 12.1 - - + -
52A VAL* 3.7 28.9 - - + -
56A GLU* 4.7 12.1 - - + +
59A PHE* 3.6 56.3 - - + -
64A VAL 3.6 1.5 + - - +
65A LYS* 1.3 76.7 - - - +
67A ILE* 1.3 63.8 + - - +
95A PRO 5.4 4.0 + - - +
96A TYR* 3.1 35.5 - - + +
97A PRO* 3.4 7.1 - - - +
153A PHE* 6.3 1.3 - - + -
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Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.9 22.7 - - + -
23A PHE* 4.3 9.4 - - + -
26A TRP* 3.5 33.4 - - + -
33A VAL 2.9 16.9 + - - +
34A LEU* 3.2 24.7 - - + +
35A PHE* 2.9 37.4 + - - -
66A LEU* 1.3 76.1 - - - +
68A ALA* 1.4 65.7 + - - +
96A TYR* 4.5 0.4 - - - -
97A PRO* 3.8 33.7 - - + +
99A ILE* 3.7 19.3 - - + -
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.6 0.2 - - - -
35A PHE* 3.2 32.2 - - + +
37A HIS* 4.8 1.8 - - + -
49A LEU* 4.2 9.0 - - + -
67A ILE* 1.4 77.3 - - - +
69A LEU* 1.3 64.9 + - - +
96A TYR* 3.9 12.1 - - + -
97A PRO 3.1 12.3 + - - +
98A ILE* 3.5 18.8 - - + -
99A ILE* 2.9 23.7 + - - +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.1 17.0 - - + -
35A PHE 2.9 10.8 + - - +
36A SER* 3.1 10.1 - - - -
37A HIS* 3.0 31.5 + - - -
68A ALA* 1.3 78.5 - - - +
70A SER* 1.3 74.5 + - - +
98A ILE* 4.3 0.2 - - - -
99A ILE* 3.6 39.0 - - + -
101A ASP* 4.0 8.3 - - + -
106A LEU* 3.8 20.9 - - + -
112A MET* 3.7 31.9 - - + -
126A THR* 3.7 15.7 - - + -
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A HIS* 3.1 39.6 - - - -
38A PRO 4.3 4.7 - - - -
40A ASP* 3.3 3.6 + - - -
69A LEU* 1.3 83.1 - - - +
71A CYS* 1.3 54.4 + - - +
72A ASP* 3.2 17.9 + - - -
77A HIS* 3.2 18.3 + - - -
99A ILE 3.2 10.5 + - - +
100A ALA* 3.5 0.7 - - - -
101A ASP* 2.7 30.4 + - - +
126A THR* 4.3 0.9 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il